# Source code for MDAnalysis.selections.charmm

    # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
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    # Please cite your use of MDAnalysis in published work:
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    # R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
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    # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
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    """
    CHARMM selections
    =================

    Write :class:`MDAnalysis.core.groups.AtomGroup` selection to a `str` file
    that defines a `CHARMM selection`_. To be used in CHARMM_ like this::

      stream macro.str

    The selection is named *mdanalysis001*.

    .. autoclass:: SelectionWriter
       :inherited-members:

    .. _CHARMM: http://www.charmm.org
    .. _CHARMM selection: http://www.charmm.org/documentation/c34b1/select.html
    """
    from . import base

    class SelectionWriter(base.SelectionWriterBase):
        format = ["CHARMM", "str"]
        ext = "str"
        continuation = "-"
        commentfmt = "! %s"
        default_numterms = (
            4  # be conservative because CHARMM only reads 72 columns
        )

        def _translate(self, atoms, **kwargs):
            # CHARMM index is 1-based
            def _index(atom):
                return "BYNUM {0:d}".format((atom.index + 1))

            return base.join(atoms, " .or.", _index)

        def _write_head(self, out, **kwargs):
            out.write(self.comment("MDAnalysis CHARMM selection"))
            out.write(
                "DEFINE {name!s} SELECT ".format(**kwargs)
                + self.continuation
                + "\n"
            )

        def _write_tail(self, out, **kwargs):
            out.write("END")